@journeyman when binding the 'start' button will be your p1 start, and the select button will be your coin button. i don't know any shootemups that use more than 4 buttons.
Problem Solved:
It turns out it was a wiring problem: the A and B Buttons were crossed on the 2nd controller. It seems the system has no way of differentiating between the two otherwise identical controllers. So the config for controller 2 probably overwrote the config for controller 1 and vice versa each time a new controller config was put in.
Not sure if this helps. I had problem where the 2:nd player use the P1 controls.
. Needed to add:
usbhid.quirks=0x16c0:0x05e1:0x040
To the /boot/cmdline.txt to get the player 2 control to be detected. Not sure if this is related at all.
@onsmike Yes, it seems a keyboard is needed. That's what "solved" the problem for me when I tried it last night at any rate. It's a bit annoying, but it works on the roms I tried.
Thanks Gerald. This worked for me! I'm assuming I'll have to do this for every additional controller I have connected, but it's not a big deal. I wonder why the main Configure Input on the emulation station doesn't work for the individual roms.